## The number of loci caught by each filter. ## ipyrad API location: [assembly].stats_dfs.s7_filters total_filters applied_order retained_loci total_prefiltered_loci 0 0 52188 filtered_by_rm_duplicates 449 449 51739 filtered_by_max_indels 8219 8219 43520 filtered_by_max_SNPs 5 1 43519 filtered_by_max_shared_het 4483 3508 40011 filtered_by_min_sample 14022 14022 25989 total_filtered_loci 27178 26199 25989 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage 07089_C18_5 9788 07141_C20_16 15474 07433_A94_38 19888 07508_C33_6 9695 07548_M28_34 16392 07551_M10_22 10695 07572_M19_3 10149 07576_C19_19 11452 07587_M10_11 64 07614_A69_41 14366 07632_C23_9 7131 07644_M20_10 8052 07646_A926_12 13529 07663_C23_8 13184 07691_M32_7 6819 07868_M9_23 8866 07869_M20_40 17706 07870_M18_17 11926 07873_M34_14 12609 07874_M3_36 14689 07877_M1_33 16323 47001_A92b_39 19491 85785_M12_24 8463 85861_M11_35 17523 ## The number of loci for which N taxa have data. ## ipyrad API location: [assembly].stats_dfs.s7_loci locus_coverage sum_coverage 1 0 0 2 0 0 3 0 0 4 3105 3105 5 2342 5447 6 2073 7520 7 1671 9191 8 1616 10807 9 1330 12137 10 1425 13562 11 1210 14772 12 1146 15918 13 1093 17011 14 1087 18098 15 967 19065 16 909 19974 17 829 20803 18 852 21655 19 727 22382 20 827 23209 21 796 24005 22 833 24838 23 1125 25963 24 26 25989 The distribution of SNPs (var and pis) per locus. ## var = Number of loci with n variable sites (pis + autapomorphies) ## pis = Number of loci with n parsimony informative site (minor allele in >1 sample) ## ipyrad API location: [assembly].stats_dfs.s7_snps ## The "reference" sample is included if present unless 'exclude_reference=True' var sum_var pis sum_pis 0 1387 0 4739 0 1 1475 1475 3469 3469 2 1628 4731 2937 9343 3 1530 9321 2412 16579 4 1545 15501 1993 24551 5 1548 23241 1705 33076 6 1465 32031 1445 41746 7 1374 41649 1204 50174 8 1323 52233 1086 58862 9 1153 62610 884 66818 10 1104 73650 727 74088 11 1033 85013 618 80886 12 971 96665 536 87318 13 843 107624 455 93233 14 782 118572 357 98231 15 678 128742 265 102206 16 689 139766 251 106222 17 628 150442 218 109928 18 558 160486 146 112556 19 491 169815 146 115330 20 433 178475 101 117350 21 412 187127 74 118904 22 357 194981 54 120092 23 336 202709 40 121012 24 308 210101 38 121924 25 275 216976 19 122399 26 228 222904 16 122815 27 221 228871 16 123247 28 206 234639 10 123527 29 171 239598 8 123759 30 135 243648 10 124059 31 116 247244 2 124121 32 107 250668 3 124217 33 98 253902 2 124283 34 55 255772 2 124351 35 62 257942 1 124386 36 61 260138 0 124386 37 32 261322 0 124386 38 27 262348 0 124386 39 23 263245 0 124386 40 28 264365 0 124386 41 22 265267 0 124386 42 17 265981 0 124386 43 13 266540 0 124386 44 13 267112 0 124386 45 4 267292 0 124386 46 3 267430 0 124386 47 7 267759 0 124386 48 0 267759 0 124386 49 5 268004 0 124386 50 4 268204 0 124386 51 0 268204 0 124386 52 0 268204 0 124386 53 2 268310 0 124386 54 1 268364 0 124386 55 1 268419 0 124386 56 0 268419 0 124386 57 1 268476 0 124386 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly 07089_C18_5 7 359936 357072 51613 18255 0.009840 0.000824 17863 9788 07141_C20_16 7 684067 678699 63285 27965 0.009392 0.000727 27449 15474 07433_A94_38 7 1494142 1484071 76647 38057 0.009557 0.000624 37427 19888 07508_C33_6 7 353763 351059 51054 18181 0.009670 0.000801 17748 9695 07548_M28_34 7 743949 737813 65291 29482 0.009682 0.000678 28923 16392 07551_M10_22 7 412435 409447 53340 19806 0.009437 0.000825 19375 10695 07572_M19_3 7 377632 374827 51338 18715 0.009636 0.000781 18309 10149 07576_C19_19 7 484159 481009 58240 21486 0.009720 0.000719 21086 11452 07587_M10_11 7 13656 13542 6993 177 0.011192 0.001259 161 64 07614_A69_41 7 599493 594617 61039 25806 0.009775 0.000697 25306 14366 07632_C23_9 7 283059 280856 48010 13836 0.009245 0.000934 13514 7131 07644_M20_10 7 297777 295670 47608 15396 0.009824 0.000881 15042 8052 07646_A926_12 7 650543 645846 67626 25088 0.009301 0.000684 24637 13529 07663_C23_8 7 568818 565230 61035 24100 0.009595 0.000697 23652 13184 07691_M32_7 7 268632 266652 44927 13451 0.009847 0.000884 13116 6819 07868_M9_23 7 326790 324379 49864 16637 0.009727 0.000815 16245 8866 07869_M20_40 7 858072 851688 65788 31756 0.009483 0.000735 31161 17706 07870_M18_17 7 494477 490695 52435 21675 0.009756 0.000723 21226 11926 07873_M34_14 7 480108 476315 56446 22798 0.009844 0.000786 22304 12609 07874_M3_36 7 725779 720155 62224 26687 0.009701 0.000656 26193 14689 07877_M1_33 7 764686 758959 66595 29474 0.009673 0.000678 28929 16323 47001_A92b_39 7 1259180 1249861 75765 37018 0.009680 0.000645 36362 19491 85785_M12_24 7 312171 309516 49012 15920 0.009914 0.000815 15536 8463 85861_M11_35 7 930771 923305 70794 32101 0.009659 0.000655 31512 17523 ## Alignment matrix statistics: snps matrix size: (24, 268476), 43.22% missing sites. sequence matrix size: (24, 5716332), 50.47% missing sites.